Solexa's Metagenomics Dataset Resource

foolishbrat · 04-08-2009, 02:07 AM

Dear all,

Is there any repository where we can download
real metagenomic reads from Solexa (i.e. not simulated dataset)?

Typically they are reads from several bacteria
or virus with the quality score in it.

- G.V

swbarnes2 · 04-08-2009, 09:47 AM

The Illumina is not the platform of choice for metagenomics right now. People prefer the longer contiguous reads of 454. So there may not be much out there.

acnoll · 04-09-2009, 08:01 AM

You might trying browsing to see whats available in the three main short read archives (contain data from 454, solexa, ABI and perhaps even other SR platforms)

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi
http://www.ebi.ac.uk/embl/Documentation/ENA-Reads.html
http://www.ddbj.nig.ac.jp/sub/trace_sra-e.html

I am not for certain but I believe data is shared between them so maybe one is as good as the other.

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04-08-2009, 02:07 AM	#1
foolishbrat Member Location: South East Asia Join Date: Nov 2008 Posts: 44	Solexa's Metagenomics Dataset Resource Dear all, Is there any repository where we can download real metagenomic reads from Solexa (i.e. not simulated dataset)? Typically they are reads from several bacteria or virus with the quality score in it. - G.V Last edited by foolishbrat; 04-08-2009 at 02:10 AM.

04-08-2009, 09:47 AM	#2
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	The Illumina is not the platform of choice for metagenomics right now. People prefer the longer contiguous reads of 454. So there may not be much out there.

04-09-2009, 08:01 AM	#3
acnoll Member Location: Kansas City Join Date: Mar 2008 Posts: 14	You might trying browsing to see whats available in the three main short read archives (contain data from 454, solexa, ABI and perhaps even other SR platforms) http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi http://www.ebi.ac.uk/embl/Documentation/ENA-Reads.html http://www.ddbj.nig.ac.jp/sub/trace_sra-e.html I am not for certain but I believe data is shared between them so maybe one is as good as the other.